Starting phenix.real_space_refine on Tue Jan 21 20:40:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dwe_47241/01_2025/9dwe_47241_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dwe_47241/01_2025/9dwe_47241.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dwe_47241/01_2025/9dwe_47241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dwe_47241/01_2025/9dwe_47241.map" model { file = "/net/cci-nas-00/data/ceres_data/9dwe_47241/01_2025/9dwe_47241_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dwe_47241/01_2025/9dwe_47241_neut.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 90 5.16 5 C 10899 2.51 5 N 2970 2.21 5 O 3438 1.98 5 H 3 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 17400 Number of models: 1 Model: "" Number of chains: 15 Chain: "L" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 807 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "H" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 907 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "A" Number of atoms: 3987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3987 Classifications: {'peptide': 499} Link IDs: {'PTRANS': 20, 'TRANS': 478} Chain breaks: 1 Chain: "M" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 807 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "I" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 907 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "B" Number of atoms: 3984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3984 Classifications: {'peptide': 499} Link IDs: {'PTRANS': 20, 'TRANS': 478} Chain breaks: 1 Chain: "N" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 807 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "J" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 907 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "C" Number of atoms: 3984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3984 Classifications: {'peptide': 499} Link IDs: {'PTRANS': 20, 'TRANS': 478} Chain breaks: 1 Chain: "P" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'GAL': 1, 'SIA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'GAL': 1, 'SIA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'GAL': 1, 'SIA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N SER H 17 " occ=0.59 ... (4 atoms not shown) pdb=" OG SER H 17 " occ=0.59 residue: pdb=" N SER H 24 " occ=0.85 ... (4 atoms not shown) pdb=" OG SER H 24 " occ=0.85 residue: pdb=" N SER I 17 " occ=0.56 ... (4 atoms not shown) pdb=" OG SER I 17 " occ=0.56 residue: pdb=" N SER I 24 " occ=0.79 ... (4 atoms not shown) pdb=" OG SER I 24 " occ=0.79 residue: pdb=" N SER J 17 " occ=0.54 ... (4 atoms not shown) pdb=" OG SER J 17 " occ=0.54 residue: pdb=" N SER J 24 " occ=0.83 ... (4 atoms not shown) pdb=" OG SER J 24 " occ=0.83 Time building chain proxies: 9.32, per 1000 atoms: 0.54 Number of scatterers: 17400 At special positions: 0 Unit cell: (134.125, 129.05, 146.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 90 16.00 O 3438 8.00 N 2970 7.00 C 10899 6.00 H 3 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS A 476 " distance=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 77 " distance=2.02 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 145 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 312 " distance=2.03 Simple disulfide: pdb=" SG CYS A 483 " - pdb=" SG CYS A 487 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 476 " distance=2.03 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 77 " distance=2.02 Simple disulfide: pdb=" SG CYS B 100 " - pdb=" SG CYS B 145 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 312 " distance=2.03 Simple disulfide: pdb=" SG CYS B 483 " - pdb=" SG CYS B 487 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS C 476 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 284 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 77 " distance=2.02 Simple disulfide: pdb=" SG CYS C 100 " - pdb=" SG CYS C 145 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 312 " distance=2.03 Simple disulfide: pdb=" SG CYS C 483 " - pdb=" SG CYS C 487 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA2-3 " GAL D 1 " - " SIA D 2 " ~> Even though SIA is an alpha isomer, a beta linkage is required... " GAL E 1 " - " SIA E 2 " " GAL P 1 " - " SIA P 2 " NAG-ASN " NAG A 601 " - " ASN A 21 " " NAG A 602 " - " ASN A 33 " " NAG A 603 " - " ASN A 175 " " NAG A 604 " - " ASN A 296 " " NAG A 605 " - " ASN A 493 " " NAG B 601 " - " ASN B 21 " " NAG B 602 " - " ASN B 33 " " NAG B 603 " - " ASN B 175 " " NAG B 604 " - " ASN B 296 " " NAG B 605 " - " ASN B 493 " " NAG C 601 " - " ASN C 21 " " NAG C 602 " - " ASN C 33 " " NAG C 603 " - " ASN C 175 " " NAG C 604 " - " ASN C 296 " " NAG C 605 " - " ASN C 493 " Time building additional restraints: 4.41 Conformation dependent library (CDL) restraints added in 2.2 seconds 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4002 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 54 sheets defined 20.5% alpha, 32.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.12 Creating SS restraints... Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'A' and resid 66 through 73 Processing helix chain 'A' and resid 74 through 81 removed outlier: 4.009A pdb=" N ASP A 78 " --> pdb=" O PRO A 75 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N GLU A 79 " --> pdb=" O MET A 76 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 81 " --> pdb=" O ASP A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 115 Processing helix chain 'A' and resid 128 through 132 Processing helix chain 'A' and resid 193 through 202 Processing helix chain 'A' and resid 376 through 398 removed outlier: 3.590A pdb=" N MET A 398 " --> pdb=" O ILE A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 466 Processing helix chain 'A' and resid 484 through 493 Processing helix chain 'A' and resid 497 through 513 removed outlier: 4.019A pdb=" N TYR A 501 " --> pdb=" O ASP A 497 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N GLU A 503 " --> pdb=" O PRO A 499 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N GLU A 504 " --> pdb=" O GLN A 500 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'B' and resid 66 through 73 Processing helix chain 'B' and resid 74 through 81 removed outlier: 3.933A pdb=" N ASP B 78 " --> pdb=" O PRO B 75 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N GLU B 79 " --> pdb=" O MET B 76 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE B 81 " --> pdb=" O ASP B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 115 Processing helix chain 'B' and resid 128 through 132 removed outlier: 3.694A pdb=" N TRP B 132 " --> pdb=" O LYS B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 201 Processing helix chain 'B' and resid 376 through 398 removed outlier: 3.646A pdb=" N MET B 398 " --> pdb=" O ILE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 466 Processing helix chain 'B' and resid 484 through 493 Processing helix chain 'B' and resid 501 through 513 Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.677A pdb=" N ASP N 82 " --> pdb=" O GLN N 79 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU N 83 " --> pdb=" O SER N 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 79 through 83' Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'C' and resid 66 through 73 Processing helix chain 'C' and resid 74 through 81 removed outlier: 4.012A pdb=" N ASP C 78 " --> pdb=" O PRO C 75 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N GLU C 79 " --> pdb=" O MET C 76 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE C 81 " --> pdb=" O ASP C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 115 Processing helix chain 'C' and resid 128 through 132 removed outlier: 3.660A pdb=" N TRP C 132 " --> pdb=" O LYS C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 201 Processing helix chain 'C' and resid 376 through 398 removed outlier: 3.601A pdb=" N MET C 398 " --> pdb=" O ILE C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 412 No H-bonds generated for 'chain 'C' and resid 410 through 412' Processing helix chain 'C' and resid 413 through 466 Processing helix chain 'C' and resid 484 through 493 Processing helix chain 'C' and resid 497 through 513 removed outlier: 3.988A pdb=" N TYR C 501 " --> pdb=" O ASP C 497 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLU C 503 " --> pdb=" O PRO C 499 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N GLU C 504 " --> pdb=" O GLN C 500 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.651A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.651A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.619A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.527A pdb=" N VAL H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 370 through 375 removed outlier: 3.965A pdb=" N ASN A 367 " --> pdb=" O GLY A 370 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY A 362 " --> pdb=" O GLY A 16 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA9, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AB1, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AB2, first strand: chain 'A' and resid 51 through 54 removed outlier: 6.880A pdb=" N LEU A 51 " --> pdb=" O GLY A 282 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N CYS A 284 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 60 through 61 removed outlier: 6.585A pdb=" N LEU A 60 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE A 89 " --> pdb=" O MET A 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 103 through 105 removed outlier: 6.480A pdb=" N SER A 104 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N TRP A 240 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LEU A 185 " --> pdb=" O TYR A 262 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N TYR A 262 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N HIS A 120 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LYS A 269 " --> pdb=" O ILE A 118 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE A 118 " --> pdb=" O LYS A 269 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 103 through 105 removed outlier: 6.480A pdb=" N SER A 104 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N TRP A 240 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N LEU A 185 " --> pdb=" O PRO A 260 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 135 through 136 Processing sheet with id=AB7, first strand: chain 'A' and resid 142 through 147 removed outlier: 4.631A pdb=" N CYS A 145 " --> pdb=" O SER A 152 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 170 through 175 Processing sheet with id=AB9, first strand: chain 'A' and resid 294 through 295 removed outlier: 4.018A pdb=" N CYS A 288 " --> pdb=" O ILE A 295 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 9 through 13 removed outlier: 6.660A pdb=" N VAL M 11 " --> pdb=" O THR M 105 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLN M 37 " --> pdb=" O LEU M 46 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N LEU M 46 " --> pdb=" O GLN M 37 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 9 through 13 removed outlier: 6.660A pdb=" N VAL M 11 " --> pdb=" O THR M 105 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 19 through 24 Processing sheet with id=AC4, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AC5, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.618A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.533A pdb=" N VAL I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 370 through 375 removed outlier: 3.504A pdb=" N GLY B 362 " --> pdb=" O GLY B 16 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AC9, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AD1, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AD2, first strand: chain 'B' and resid 51 through 54 removed outlier: 6.860A pdb=" N LEU B 51 " --> pdb=" O GLY B 282 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N CYS B 284 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 60 through 61 removed outlier: 6.606A pdb=" N LEU B 60 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE B 89 " --> pdb=" O MET B 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.528A pdb=" N SER B 104 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N TRP B 240 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N LEU B 185 " --> pdb=" O TYR B 262 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N TYR B 262 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N HIS B 120 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LYS B 269 " --> pdb=" O ILE B 118 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE B 118 " --> pdb=" O LYS B 269 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.528A pdb=" N SER B 104 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N TRP B 240 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N LEU B 185 " --> pdb=" O PRO B 260 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 135 through 136 Processing sheet with id=AD7, first strand: chain 'B' and resid 142 through 147 removed outlier: 4.644A pdb=" N CYS B 145 " --> pdb=" O SER B 152 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 170 through 175 Processing sheet with id=AD9, first strand: chain 'B' and resid 288 through 289 Processing sheet with id=AE1, first strand: chain 'N' and resid 9 through 13 removed outlier: 6.641A pdb=" N VAL N 11 " --> pdb=" O THR N 105 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N GLN N 37 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LEU N 46 " --> pdb=" O GLN N 37 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'N' and resid 9 through 13 removed outlier: 6.641A pdb=" N VAL N 11 " --> pdb=" O THR N 105 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AE4, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AE5, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.623A pdb=" N GLY J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.524A pdb=" N VAL J 102 " --> pdb=" O ARG J 94 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 372 through 375 removed outlier: 3.518A pdb=" N GLY C 362 " --> pdb=" O GLY C 16 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AE9, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AF1, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AF2, first strand: chain 'C' and resid 51 through 54 removed outlier: 6.867A pdb=" N LEU C 51 " --> pdb=" O GLY C 282 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N CYS C 284 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 60 through 61 removed outlier: 6.595A pdb=" N LEU C 60 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE C 89 " --> pdb=" O MET C 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'C' and resid 103 through 105 removed outlier: 6.482A pdb=" N SER C 104 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N TRP C 240 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N LEU C 185 " --> pdb=" O TYR C 262 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TYR C 262 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N HIS C 120 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LYS C 269 " --> pdb=" O ILE C 118 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE C 118 " --> pdb=" O LYS C 269 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 103 through 105 removed outlier: 6.482A pdb=" N SER C 104 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N TRP C 240 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N LEU C 185 " --> pdb=" O PRO C 260 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 135 through 136 Processing sheet with id=AF7, first strand: chain 'C' and resid 142 through 147 removed outlier: 4.639A pdb=" N CYS C 145 " --> pdb=" O SER C 152 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 170 through 175 Processing sheet with id=AF9, first strand: chain 'C' and resid 288 through 289 747 hydrogen bonds defined for protein. 1935 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.84 Time building geometry restraints manager: 4.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.01 - 1.17: 3 1.17 - 1.33: 5026 1.33 - 1.49: 5544 1.49 - 1.66: 7082 1.66 - 1.82: 132 Bond restraints: 17787 Sorted by residual: bond pdb=" N GLY A 340 " pdb=" H GLY A 340 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" CA GLY A 340 " pdb=" HA3 GLY A 340 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.61e+01 bond pdb=" CA GLY A 340 " pdb=" HA2 GLY A 340 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" C1 SIA P 2 " pdb=" O1A SIA P 2 " ideal model delta sigma weight residual 1.262 1.197 0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" C1 SIA E 2 " pdb=" O1A SIA E 2 " ideal model delta sigma weight residual 1.262 1.197 0.065 2.00e-02 2.50e+03 1.06e+01 ... (remaining 17782 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 23486 2.12 - 4.24: 558 4.24 - 6.35: 39 6.35 - 8.47: 17 8.47 - 10.59: 11 Bond angle restraints: 24111 Sorted by residual: angle pdb=" C SER N 2 " pdb=" N ALA N 3 " pdb=" CA ALA N 3 " ideal model delta sigma weight residual 121.54 128.70 -7.16 1.91e+00 2.74e-01 1.40e+01 angle pdb=" C SER M 2 " pdb=" N ALA M 3 " pdb=" CA ALA M 3 " ideal model delta sigma weight residual 121.54 128.69 -7.15 1.91e+00 2.74e-01 1.40e+01 angle pdb=" C SER L 2 " pdb=" N ALA L 3 " pdb=" CA ALA L 3 " ideal model delta sigma weight residual 121.54 128.68 -7.14 1.91e+00 2.74e-01 1.40e+01 angle pdb=" C1 SIA P 2 " pdb=" C2 SIA P 2 " pdb=" C3 SIA P 2 " ideal model delta sigma weight residual 115.48 104.89 10.59 3.00e+00 1.11e-01 1.25e+01 angle pdb=" CA ARG C 117 " pdb=" CB ARG C 117 " pdb=" CG ARG C 117 " ideal model delta sigma weight residual 114.10 121.03 -6.93 2.00e+00 2.50e-01 1.20e+01 ... (remaining 24106 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.52: 10419 26.52 - 53.05: 421 53.05 - 79.57: 52 79.57 - 106.09: 14 106.09 - 132.62: 1 Dihedral angle restraints: 10907 sinusoidal: 4628 harmonic: 6279 Sorted by residual: dihedral pdb=" C9 SIA E 2 " pdb=" C7 SIA E 2 " pdb=" C8 SIA E 2 " pdb=" O7 SIA E 2 " ideal model delta sinusoidal sigma weight residual -44.94 87.68 -132.62 1 3.00e+01 1.11e-03 1.79e+01 dihedral pdb=" CB CYS I 22 " pdb=" SG CYS I 22 " pdb=" SG CYS I 92 " pdb=" CB CYS I 92 " ideal model delta sinusoidal sigma weight residual 93.00 57.68 35.32 1 1.00e+01 1.00e-02 1.77e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual 93.00 58.04 34.96 1 1.00e+01 1.00e-02 1.73e+01 ... (remaining 10904 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 2575 0.120 - 0.240: 60 0.240 - 0.359: 3 0.359 - 0.479: 4 0.479 - 0.599: 1 Chirality restraints: 2643 Sorted by residual: chirality pdb=" C2 SIA P 2 " pdb=" O3 GAL P 1 " pdb=" C1 SIA P 2 " pdb=" O6 SIA P 2 " both_signs ideal model delta sigma weight residual False -2.50 -2.83 0.33 2.00e-02 2.50e+03 2.70e+02 chirality pdb=" C2 SIA D 2 " pdb=" O3 GAL D 1 " pdb=" C1 SIA D 2 " pdb=" O6 SIA D 2 " both_signs ideal model delta sigma weight residual False -2.50 -2.83 0.33 2.00e-02 2.50e+03 2.69e+02 chirality pdb=" C2 SIA E 2 " pdb=" O3 GAL E 1 " pdb=" C1 SIA E 2 " pdb=" O6 SIA E 2 " both_signs ideal model delta sigma weight residual False -2.50 -2.74 0.24 2.00e-02 2.50e+03 1.46e+02 ... (remaining 2640 not shown) Planarity restraints: 3135 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 SIA P 2 " 0.016 2.00e-02 2.50e+03 4.79e-02 2.86e+01 pdb=" C11 SIA P 2 " -0.044 2.00e-02 2.50e+03 pdb=" C5 SIA P 2 " -0.058 2.00e-02 2.50e+03 pdb=" N5 SIA P 2 " 0.076 2.00e-02 2.50e+03 pdb=" O10 SIA P 2 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 290 " 0.046 5.00e-02 4.00e+02 7.03e-02 7.90e+00 pdb=" N PRO C 291 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO C 291 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 291 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C10 SIA D 2 " 0.007 2.00e-02 2.50e+03 2.42e-02 7.31e+00 pdb=" C11 SIA D 2 " -0.022 2.00e-02 2.50e+03 pdb=" C5 SIA D 2 " -0.029 2.00e-02 2.50e+03 pdb=" N5 SIA D 2 " 0.039 2.00e-02 2.50e+03 pdb=" O10 SIA D 2 " 0.006 2.00e-02 2.50e+03 ... (remaining 3132 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.11: 3 2.11 - 2.73: 1099 2.73 - 3.35: 18934 3.35 - 3.98: 38221 3.98 - 4.60: 53340 Nonbonded interactions: 111597 Sorted by model distance: nonbonded pdb=" O SER B 513 " pdb=" CZ ARG C 506 " model vdw 1.485 3.100 nonbonded pdb=" O SER B 513 " pdb=" NH1 ARG C 506 " model vdw 1.624 2.950 nonbonded pdb=" O SER B 513 " pdb=" NE ARG C 506 " model vdw 1.921 2.950 nonbonded pdb=" OH TYR A 101 " pdb=" O9 SIA E 2 " model vdw 2.279 2.800 nonbonded pdb=" OG1 THR B 290 " pdb=" O GLY B 293 " model vdw 2.279 2.800 ... (remaining 111592 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 332 or (resid 340 and (name N or name CA or name \ C or name O )) or resid 341 through 513 or resid 601 through 605)) selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'P' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.54 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 26.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 42.300 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 17784 Z= 0.312 Angle : 0.756 10.591 24105 Z= 0.395 Chirality : 0.054 0.599 2643 Planarity : 0.006 0.070 3120 Dihedral : 14.212 132.617 6831 Min Nonbonded Distance : 1.485 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.17), residues: 2163 helix: -0.46 (0.23), residues: 396 sheet: -0.06 (0.21), residues: 615 loop : -0.78 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 70 HIS 0.009 0.001 HIS B 450 PHE 0.032 0.002 PHE C 121 TYR 0.013 0.002 TYR A 496 ARG 0.006 0.001 ARG B 407 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 412 time to evaluate : 1.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8466 (mt0) cc_final: 0.8064 (tt0) REVERT: A 287 LYS cc_start: 0.8198 (mttm) cc_final: 0.7788 (mptt) REVERT: A 311 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8277 (mm-30) REVERT: A 507 LEU cc_start: 0.8018 (tp) cc_final: 0.7772 (mp) REVERT: M 79 GLN cc_start: 0.6832 (mm-40) cc_final: 0.6547 (mt0) REVERT: I 3 GLN cc_start: 0.8453 (mt0) cc_final: 0.7994 (tt0) REVERT: B 287 LYS cc_start: 0.8108 (mttm) cc_final: 0.7713 (mptt) REVERT: B 311 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8220 (mm-30) REVERT: B 392 ASN cc_start: 0.8336 (m-40) cc_final: 0.8043 (m-40) REVERT: B 414 ARG cc_start: 0.8550 (mmm160) cc_final: 0.8273 (mtm180) REVERT: B 470 LYS cc_start: 0.8224 (ttpt) cc_final: 0.7362 (tttt) REVERT: B 500 GLN cc_start: 0.7953 (mt0) cc_final: 0.7745 (tt0) REVERT: B 508 LYS cc_start: 0.7429 (tttm) cc_final: 0.6812 (mmmt) REVERT: J 3 GLN cc_start: 0.8474 (mt0) cc_final: 0.7905 (mp10) REVERT: C 287 LYS cc_start: 0.8136 (mttm) cc_final: 0.7674 (mptt) REVERT: C 311 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8173 (mm-30) REVERT: C 414 ARG cc_start: 0.8290 (mmt-90) cc_final: 0.8050 (mtm180) REVERT: C 417 GLU cc_start: 0.8628 (tt0) cc_final: 0.8347 (tt0) REVERT: C 501 TYR cc_start: 0.8740 (m-80) cc_final: 0.8227 (m-80) outliers start: 0 outliers final: 0 residues processed: 412 average time/residue: 1.3724 time to fit residues: 628.6499 Evaluate side-chains 250 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 2.9990 chunk 163 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 196 optimal weight: 0.3980 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN A 230 ASN A 250 HIS A 364 HIS A 365 HIS A 389 ASN ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 ASN B 399 ASN ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 ASN ** C 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 500 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.158867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.127213 restraints weight = 19386.537| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.85 r_work: 0.3427 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3271 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3271 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 17784 Z= 0.489 Angle : 0.650 7.687 24105 Z= 0.332 Chirality : 0.053 0.475 2643 Planarity : 0.005 0.064 3120 Dihedral : 8.078 128.775 2826 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.21 % Allowed : 10.49 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.17), residues: 2163 helix: 0.39 (0.25), residues: 390 sheet: 0.01 (0.21), residues: 576 loop : -0.73 (0.17), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 70 HIS 0.010 0.002 HIS C 302 PHE 0.023 0.003 PHE A 342 TYR 0.016 0.002 TYR I 100A ARG 0.005 0.001 ARG B 415 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 256 time to evaluate : 1.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 MET cc_start: 0.9038 (mtt) cc_final: 0.8824 (mtt) REVERT: A 287 LYS cc_start: 0.8053 (mttm) cc_final: 0.7496 (mptt) REVERT: A 311 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7904 (mm-30) REVERT: A 398 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7685 (mtp) REVERT: A 507 LEU cc_start: 0.7976 (tp) cc_final: 0.7679 (mp) REVERT: I 3 GLN cc_start: 0.8389 (mt0) cc_final: 0.7835 (tt0) REVERT: B 180 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7872 (pm20) REVERT: B 287 LYS cc_start: 0.8054 (mttm) cc_final: 0.7499 (mptt) REVERT: B 311 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7824 (mm-30) REVERT: B 414 ARG cc_start: 0.8493 (mmm160) cc_final: 0.7742 (mpp-170) REVERT: B 497 ASP cc_start: 0.8158 (OUTLIER) cc_final: 0.7955 (t0) REVERT: B 500 GLN cc_start: 0.7883 (mt0) cc_final: 0.7518 (tt0) REVERT: J 3 GLN cc_start: 0.8406 (mt0) cc_final: 0.7851 (tt0) REVERT: C 122 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7582 (tm-30) REVERT: C 193 ASN cc_start: 0.8569 (OUTLIER) cc_final: 0.8269 (p0) REVERT: C 202 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.7803 (tppt) REVERT: C 287 LYS cc_start: 0.8028 (mttm) cc_final: 0.7482 (mptt) REVERT: C 311 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7822 (mm-30) REVERT: C 398 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7730 (mtp) REVERT: C 414 ARG cc_start: 0.7983 (mmt-90) cc_final: 0.7617 (mtm180) REVERT: C 417 GLU cc_start: 0.8582 (tt0) cc_final: 0.8161 (tt0) REVERT: C 470 LYS cc_start: 0.7369 (OUTLIER) cc_final: 0.6758 (tttt) REVERT: C 501 TYR cc_start: 0.8611 (m-80) cc_final: 0.8301 (m-80) outliers start: 60 outliers final: 33 residues processed: 278 average time/residue: 1.4366 time to fit residues: 443.0807 Evaluate side-chains 267 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 226 time to evaluate : 1.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 415 ARG Chi-restraints excluded: chain C residue 470 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 101 optimal weight: 0.5980 chunk 6 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 chunk 161 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 142 optimal weight: 0.5980 chunk 169 optimal weight: 0.6980 chunk 148 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 53 GLN ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 ASN B 97 ASN B 176 ASN ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 ASN C 97 ASN ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 ASN ** C 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.160435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.128154 restraints weight = 19107.008| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.93 r_work: 0.3496 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3329 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3329 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17784 Z= 0.199 Angle : 0.482 6.802 24105 Z= 0.249 Chirality : 0.046 0.391 2643 Planarity : 0.003 0.043 3120 Dihedral : 7.552 122.514 2826 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.89 % Allowed : 12.73 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.18), residues: 2163 helix: 1.08 (0.26), residues: 396 sheet: 0.03 (0.22), residues: 558 loop : -0.54 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 431 HIS 0.004 0.001 HIS A 18 PHE 0.013 0.001 PHE A 342 TYR 0.009 0.001 TYR J 100A ARG 0.003 0.000 ARG A 506 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 260 time to evaluate : 1.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 24 SER cc_start: 0.7654 (m) cc_final: 0.7432 (p) REVERT: A 287 LYS cc_start: 0.7942 (mttm) cc_final: 0.7324 (mptt) REVERT: A 311 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7627 (mm-30) REVERT: A 482 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8161 (tptt) REVERT: A 507 LEU cc_start: 0.7842 (tp) cc_final: 0.7523 (mp) REVERT: M 69 THR cc_start: 0.8296 (p) cc_final: 0.7780 (t) REVERT: I 3 GLN cc_start: 0.8270 (mt0) cc_final: 0.7668 (tt0) REVERT: B 180 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7793 (pm20) REVERT: B 287 LYS cc_start: 0.7933 (mttm) cc_final: 0.7334 (mptt) REVERT: B 311 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7611 (mm-30) REVERT: B 414 ARG cc_start: 0.8385 (mmm160) cc_final: 0.7590 (mtm180) REVERT: B 422 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7903 (mmtp) REVERT: B 497 ASP cc_start: 0.8063 (t0) cc_final: 0.7843 (t0) REVERT: B 500 GLN cc_start: 0.7806 (mt0) cc_final: 0.7409 (tt0) REVERT: N 53 GLN cc_start: 0.7490 (mm-40) cc_final: 0.7059 (mp10) REVERT: C 76 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.8135 (mmp) REVERT: C 122 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7611 (tm-30) REVERT: C 202 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.7686 (tppt) REVERT: C 269 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.7850 (mmtm) REVERT: C 287 LYS cc_start: 0.7985 (mttm) cc_final: 0.7379 (mptt) REVERT: C 311 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7565 (mm-30) REVERT: C 398 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7730 (mtp) REVERT: C 414 ARG cc_start: 0.7741 (mmt-90) cc_final: 0.7300 (mtm180) REVERT: C 417 GLU cc_start: 0.8363 (tt0) cc_final: 0.7965 (tt0) REVERT: C 501 TYR cc_start: 0.8437 (m-80) cc_final: 0.8121 (m-80) outliers start: 54 outliers final: 29 residues processed: 282 average time/residue: 1.3658 time to fit residues: 429.0742 Evaluate side-chains 273 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 236 time to evaluate : 2.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 421 LYS Chi-restraints excluded: chain B residue 422 LYS Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 269 LYS Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 415 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 212 optimal weight: 0.7980 chunk 72 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 77 optimal weight: 0.1980 chunk 96 optimal weight: 2.9990 chunk 25 optimal weight: 0.0670 chunk 210 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 overall best weight: 1.0120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 ASN A 199 ASN ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 ASN ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 ASN C 250 HIS ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 ASN ** C 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.160414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.128913 restraints weight = 19256.712| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.85 r_work: 0.3435 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3286 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3286 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17784 Z= 0.263 Angle : 0.500 6.764 24105 Z= 0.255 Chirality : 0.047 0.454 2643 Planarity : 0.003 0.038 3120 Dihedral : 7.450 121.535 2826 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.44 % Allowed : 13.00 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.18), residues: 2163 helix: 1.30 (0.26), residues: 396 sheet: 0.16 (0.22), residues: 564 loop : -0.50 (0.17), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 431 HIS 0.006 0.001 HIS C 18 PHE 0.015 0.002 PHE A 342 TYR 0.010 0.001 TYR A 496 ARG 0.003 0.000 ARG B 415 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 246 time to evaluate : 2.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 69 THR cc_start: 0.8383 (p) cc_final: 0.7913 (t) REVERT: A 180 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7745 (pm20) REVERT: A 287 LYS cc_start: 0.8041 (mttm) cc_final: 0.7483 (mptt) REVERT: A 311 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7750 (mm-30) REVERT: A 398 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7606 (mtp) REVERT: A 482 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8190 (tptt) REVERT: A 507 LEU cc_start: 0.7957 (tp) cc_final: 0.7651 (mp) REVERT: M 69 THR cc_start: 0.8346 (p) cc_final: 0.7837 (t) REVERT: B 114 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8199 (ttp) REVERT: B 122 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.7729 (tt0) REVERT: B 180 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7869 (pm20) REVERT: B 287 LYS cc_start: 0.8063 (mttm) cc_final: 0.7482 (mptt) REVERT: B 311 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7750 (mm-30) REVERT: B 398 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7660 (mmt) REVERT: B 414 ARG cc_start: 0.8569 (mmm160) cc_final: 0.7816 (mtm180) REVERT: B 500 GLN cc_start: 0.7879 (mt0) cc_final: 0.7483 (tt0) REVERT: N 53 GLN cc_start: 0.7574 (mm-40) cc_final: 0.7145 (mp10) REVERT: C 122 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7747 (tm-30) REVERT: C 202 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.7754 (tppt) REVERT: C 287 LYS cc_start: 0.8114 (mttm) cc_final: 0.7560 (mptt) REVERT: C 398 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7748 (mtp) REVERT: C 414 ARG cc_start: 0.7958 (mmt-90) cc_final: 0.7611 (mtm180) REVERT: C 417 GLU cc_start: 0.8530 (tt0) cc_final: 0.8169 (tt0) REVERT: C 470 LYS cc_start: 0.7309 (OUTLIER) cc_final: 0.6754 (tttt) REVERT: C 501 TYR cc_start: 0.8620 (m-80) cc_final: 0.8282 (m-80) REVERT: C 506 ARG cc_start: 0.7687 (ttp80) cc_final: 0.6961 (ttp80) outliers start: 83 outliers final: 45 residues processed: 288 average time/residue: 1.3487 time to fit residues: 432.7284 Evaluate side-chains 289 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 233 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 421 LYS Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain C residue 12 GLN Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 415 ARG Chi-restraints excluded: chain C residue 423 MET Chi-restraints excluded: chain C residue 470 LYS Chi-restraints excluded: chain C residue 507 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 37 optimal weight: 0.0040 chunk 25 optimal weight: 0.3980 chunk 144 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 chunk 200 optimal weight: 0.0770 chunk 28 optimal weight: 0.0870 chunk 207 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 211 optimal weight: 0.4980 overall best weight: 0.2128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 ASN B 192 ASN B 399 ASN C 399 ASN ** C 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.163271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.129799 restraints weight = 19160.108| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.90 r_work: 0.3489 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3340 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3340 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 17784 Z= 0.110 Angle : 0.423 5.597 24105 Z= 0.219 Chirality : 0.044 0.347 2643 Planarity : 0.003 0.034 3120 Dihedral : 6.921 113.132 2826 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.19 % Allowed : 15.78 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.18), residues: 2163 helix: 1.89 (0.26), residues: 396 sheet: 0.29 (0.22), residues: 585 loop : -0.21 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.000 TRP A 431 HIS 0.002 0.000 HIS C 283 PHE 0.009 0.001 PHE A 121 TYR 0.008 0.001 TYR B 363 ARG 0.007 0.000 ARG B 506 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 263 time to evaluate : 1.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 69 THR cc_start: 0.8333 (p) cc_final: 0.7868 (t) REVERT: A 180 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7680 (pm20) REVERT: A 287 LYS cc_start: 0.8068 (mttm) cc_final: 0.7485 (mptt) REVERT: A 311 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7700 (mm-30) REVERT: A 507 LEU cc_start: 0.7927 (tp) cc_final: 0.7630 (mp) REVERT: M 53 GLN cc_start: 0.7409 (mm-40) cc_final: 0.6932 (mp10) REVERT: M 69 THR cc_start: 0.8315 (p) cc_final: 0.7821 (t) REVERT: B 122 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.7684 (tt0) REVERT: B 287 LYS cc_start: 0.8061 (mttm) cc_final: 0.7478 (mptt) REVERT: B 311 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7638 (mm-30) REVERT: B 398 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7679 (mmt) REVERT: B 414 ARG cc_start: 0.8560 (mmm160) cc_final: 0.7827 (mtm180) REVERT: B 422 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8067 (mmtp) REVERT: B 500 GLN cc_start: 0.7803 (mt0) cc_final: 0.7441 (tt0) REVERT: N 53 GLN cc_start: 0.7480 (mm-40) cc_final: 0.7041 (mp10) REVERT: C 122 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7747 (tm-30) REVERT: C 287 LYS cc_start: 0.7988 (mttm) cc_final: 0.7421 (mptt) REVERT: C 414 ARG cc_start: 0.7935 (mmt-90) cc_final: 0.7527 (mtm180) REVERT: C 417 GLU cc_start: 0.8479 (tt0) cc_final: 0.8180 (tt0) REVERT: C 501 TYR cc_start: 0.8638 (m-80) cc_final: 0.8275 (m-80) REVERT: C 506 ARG cc_start: 0.7549 (ttp80) cc_final: 0.6821 (ttp80) outliers start: 41 outliers final: 14 residues processed: 291 average time/residue: 1.3215 time to fit residues: 430.2813 Evaluate side-chains 260 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 241 time to evaluate : 1.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain B residue 421 LYS Chi-restraints excluded: chain B residue 422 LYS Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain C residue 12 GLN Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain C residue 423 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.2258 > 50: distance: 78 - 125: 18.011 distance: 83 - 88: 11.379 distance: 88 - 89: 13.142 distance: 88 - 116: 15.267 distance: 89 - 90: 10.783 distance: 89 - 92: 19.708 distance: 90 - 91: 30.464 distance: 90 - 100: 12.950 distance: 91 - 113: 21.281 distance: 92 - 93: 19.091 distance: 93 - 94: 17.385 distance: 93 - 95: 22.193 distance: 94 - 96: 17.563 distance: 95 - 97: 33.855 distance: 96 - 98: 15.707 distance: 97 - 98: 13.626 distance: 98 - 99: 8.482 distance: 100 - 101: 13.585 distance: 101 - 102: 21.412 distance: 101 - 104: 13.157 distance: 102 - 103: 38.602 distance: 102 - 109: 20.961 distance: 104 - 105: 26.439 distance: 105 - 106: 7.483 distance: 106 - 107: 6.690 distance: 106 - 108: 10.036 distance: 109 - 110: 41.771 distance: 110 - 111: 27.193 distance: 111 - 112: 33.936 distance: 111 - 113: 10.996 distance: 113 - 114: 10.617 distance: 114 - 115: 24.644 distance: 114 - 117: 40.069 distance: 115 - 116: 20.638 distance: 115 - 118: 19.391 distance: 118 - 119: 15.746 distance: 118 - 124: 24.599 distance: 119 - 120: 58.226 distance: 119 - 122: 26.555 distance: 120 - 121: 45.866 distance: 120 - 125: 50.213 distance: 122 - 123: 19.026 distance: 123 - 124: 33.459 distance: 125 - 126: 19.746 distance: 126 - 127: 16.768 distance: 126 - 129: 17.149 distance: 127 - 128: 30.920 distance: 127 - 131: 28.388 distance: 129 - 130: 9.461 distance: 131 - 132: 5.342 distance: 132 - 133: 12.371 distance: 132 - 135: 15.103 distance: 133 - 134: 9.156 distance: 133 - 142: 22.178 distance: 135 - 136: 14.078 distance: 136 - 137: 10.774 distance: 136 - 138: 8.472 distance: 137 - 139: 9.339 distance: 138 - 140: 5.842 distance: 140 - 141: 3.312 distance: 142 - 143: 16.237 distance: 143 - 144: 33.232 distance: 143 - 146: 22.644 distance: 144 - 145: 44.399 distance: 144 - 153: 19.929 distance: 146 - 147: 9.620 distance: 147 - 148: 6.369 distance: 147 - 149: 8.367 distance: 148 - 150: 8.774 distance: 149 - 151: 8.083 distance: 150 - 152: 6.845 distance: 153 - 154: 15.863 distance: 154 - 155: 30.503 distance: 154 - 157: 13.439 distance: 155 - 156: 17.053 distance: 155 - 164: 29.330 distance: 157 - 158: 39.626 distance: 158 - 159: 9.187 distance: 159 - 160: 7.310 distance: 160 - 161: 4.147 distance: 161 - 162: 4.929 distance: 161 - 163: 4.482 distance: 164 - 165: 10.571 distance: 165 - 166: 16.273 distance: 165 - 168: 19.007 distance: 166 - 167: 12.999 distance: 166 - 172: 13.573 distance: 168 - 169: 21.206 distance: 169 - 170: 30.636 distance: 169 - 171: 18.279